Help, Rain water is seeping up into the rear passenger side floorboard carpet?

Is there some sort of drain hole that is plugged?

2004 4Runner

 

My guess would be sunroof drain if you have a sunroof, I searched a couple
threads here and found a couple results but nothing on your year, I’m sure someone else will chime
in but unless some weird weatherstripping is bad and letting water in it could only be a few things if it’s coming from above.

 

I don't know about a 4Runner but Toyota likes to use rubber plugs in the floor of their passenger cars, check they're all in place. One popped out of our Yaris and the spare tire well filled with 1" of water.

 

there is a rubber plug underneath the rear passenger seat on the bottom of the floorboard. I crawled underneath and pulled the plug out and the carpet matting was wet.